When I met the POCO lineman there he checked connections and load tested, since the problem goes away when the Emergency Disconnect is shut off the problem seems to be between the Emergency disconnect and the Service disconnect in the house,Did you check the neutrals at any other houses fed by this transformer and metallic water lines?
Service disconnect is original in the SQ-D QO panel on the opposite end of the house, I have narrowed it down when I shut off all L2 breakers and create large neutral load with all L1-N breakers on, current is flowing parallel with the SE cable across the house via gas and water pipes. Same if I shut off all L1 breakers and switch on the L2. I am going to go back and look for a buried splice in the SE cable, part of the basement is finished and I cant see the entire cable as its is routed around the finished area into a crawl space. The gas pipe goes thru the finished part a shorter direct route out to the meters.
I am not the installer of the service but its new, there is new ground rod at the EM disconnect.